When you compiled antechamber, did you get warnings such as the following?
alc.c:155: warning: call to __builtin___strcpy_chk will always
overflow destination buffer
If so, this is a bug in antechamber - there are several instances
where a string is copied into a char array that is too small. Please
try the attached patch.
--Tom
2009/9/22 Alan <alanwilter.gmail.com>:
> Hi there,
>
> I would like to know if there's other already using (or trying to use)
> AmberTools with Snow Leopard in 64 bits kernel.
>
> I did a try and although I had a nice compilation (gcc/gfortran with
> -m64), running tests failed for:
>
> nab, antechamber (some cases)
>
> For example:
>
> make -f Makefile_at test.nab
> ( cd nab; make test )
> =====================================================
> Running test to make dna duplex:
>
> /bin/sh: line 1: 21844 Segmentation fault ./duplex < duplex.in
> make[1]: *** [duplex_test] Error 139
> make: *** [test.nab] Error 2
>
> make -f Makefile_at test.antechamber
> cd antechamber/top2mol2 && ./Run.top2mol2
> diffing sustiva.mol2.save with sustiva.mol2
> PASSED
> ==============================================================
> [snip]
> ==============================================================
> diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
> possible FAILURE: check fluorescein_f2.mol2.dif
> ==============================================================
> cd antechamber/c60 && ./Run.c60
> Abort
> ./Run.c60: Program error
> make: *** [test.antechamber] Error 1
>
> Many thanks in advance,
>
> Alan
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 22 2009 - 11:30:02 PDT
